JWS-112 Bumping version of T-Coffee to version 11.00.8cbe486.

[jabaws.git] / binaries / src / tcoffee / t_coffee_source / util_lib / reformat_struc.h

diff --git a/binaries/src/tcoffee/t_coffee_source/util_lib/reformat_struc.h b/binaries/src/tcoffee/t_coffee_source/util_lib/reformat_struc.h
new file mode 100644 (file)
index 0000000..55cc109
--- /dev/null
+++ b/binaries/src/tcoffee/t_coffee_source/util_lib/reformat_struc.h
@@ -0,0 +1,56 @@
+/******************************COPYRIGHT NOTICE*******************************/
+/*  (c) Centro de Regulacio Genomica                                                        */
+/*  and                                                                                     */
+/*  Cedric Notredame                                                                        */
+/*  12 Aug 2014 - 22:07.                                                                    */
+/*All rights reserved.                                                                      */
+/*This file is part of T-COFFEE.                                                            */
+/*                                                                                          */
+/*    T-COFFEE is free software; you can redistribute it and/or modify                      */
+/*    it under the terms of the GNU General Public License as published by                  */
+/*    the Free Software Foundation; either version 2 of the License, or                     */
+/*    (at your option) any later version.                                                   */
+/*                                                                                          */
+/*    T-COFFEE is distributed in the hope that it will be useful,                           */
+/*    but WITHOUT ANY WARRANTY; without even the implied warranty of                        */
+/*    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the                         */
+/*    GNU General Public License for more details.                                          */
+/*                                                                                          */
+/*    You should have received a copy of the GNU General Public License                     */
+/*    along with Foobar; if not, write to the Free Software                                 */
+/*    Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA  02111-1307  USA             */
+/*...............................................                                           */
+/*  If you need some more information                                                       */
+/*  cedric.notredame@europe.com                                                             */
+/*...............................................                                           */
+/******************************COPYRIGHT NOTICE*******************************/
+char * process_repeat (char *aln, char *seq, char *pdb);
+char     * normalize_pdb_file  (char *name, char *seq,char *out_file);
+Ca_trace * trim_ca_trace (Ca_trace *st, char *seq );
+
+Ca_trace * read_ca_trace (char *file, char *seq_field );
+Ca_trace * simple_read_ca_trace (char *file );
+Ca_trace * hasch_ca_trace             ( Ca_trace *T);
+Ca_trace * hasch_ca_trace_nb          ( Ca_trace *T);
+Ca_trace * hasch_ca_trace_bubble      ( Ca_trace *T);
+Ca_trace * hasch_ca_trace_transversal ( Ca_trace *TRACE);
+
+float get_closest_vdw_contact ( Atom *A, Atom*B);
+float get_atomic_distance ( Atom *A, Atom*B);
+int   residues2contacts (Atom *A, Atom*B, float probe);
+float ** trace2ca_distances(Ca_trace *T, float max);
+float ** trace2contacts(Ca_trace *T, float probe);
+float ** trace2best_contacts(Ca_trace *T, float probe );
+float ** trace2closest_contacts (Ca_trace *T, float probe);
+float ** trace2count_contacts(Ca_trace *T, float probe);
+
+
+float** print_contacts ( char  *file1, char *file2, float T);
+char *  map_contacts ( char  *file1, char *file2, float T);
+int * identify_contacts (Ca_trace *ST1,Ca_trace *ST2, float T);
+Sequence *seq2contacts4lignads ( Sequence *S, float T);
+char *string2contacts (char *seq,char *name,char *comment, float T);
+char **struc2nb (char *name,char *seq, char *comment, float Threshold, char *atom_list, char *output);
+char **struclist2nb (char *name,char *seq, char *comment, float Threshold, char *atom_list, char *output);
+
+float atom2radius (char *t);